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Yorodumi- PDB-3wtp: Crystal Structure of the heterotypic nucleosome containing human ... -
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-Basic information
Entry | Database: PDB / ID: 3wtp | ||||||
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Title | Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / histone fold / DNA binding / chromatin formation / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of chromosome condensation / CENP-A containing chromatin assembly / Barr body / regulation of centromere complex assembly / muscle cell differentiation / protein localization to chromosome, centromeric region / kinetochore assembly / pericentric heterochromatin formation / inner kinetochore / condensed chromosome, centromeric region ...negative regulation of chromosome condensation / CENP-A containing chromatin assembly / Barr body / regulation of centromere complex assembly / muscle cell differentiation / protein localization to chromosome, centromeric region / kinetochore assembly / pericentric heterochromatin formation / inner kinetochore / condensed chromosome, centromeric region / oocyte maturation / nucleus organization / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic cytokinesis / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / single fertilization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / RNA polymerase II core promoter sequence-specific DNA binding / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / telomere organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Resolution of Sister Chromatid Cohesion / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / structural constituent of chromatin / Separation of Sister Chromatids / male gonad development / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / HATs acetylate histones / antibacterial humoral response / chromosome, telomeric region / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Arimura, Y. / Shirayama, K. / Horikoshi, N. / Fujita, R. / Kagawa, W. / Fukagawa, T. / Almouzni, G. / Kurumizaka, H. | ||||||
Citation | Journal: Sci Rep / Year: 2014 Title: Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3 Authors: Arimura, Y. / Shirayama, K. / Horikoshi, N. / Fujita, R. / Taguchi, H. / Kagawa, W. / Fukagawa, T. / Almouzni, G. / Kurumizaka, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wtp.cif.gz | 318.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wtp.ent.gz | 241.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wtp_validation.pdf.gz | 500.3 KB | Display | wwPDB validaton report |
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Full document | 3wtp_full_validation.pdf.gz | 517.2 KB | Display | |
Data in XML | 3wtp_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 3wtp_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wtp ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wtp | HTTPS FTP |
-Related structure data
Related structure data | 2cv5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 5 types, 8 molecules ABFCGDHE
#1: Protein | Mass: 16305.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P49450 | ||||||
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#2: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H3.3, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, ...Gene: H3.3, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4 Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62805 #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFA, H2AFM, H4, HIST1H2AB, HIST1H2AE / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P04908 #4: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2A, H2BFR, HIST1H2BJ / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899 #5: Protein | | Mass: 15710.351 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84243 |
-DNA chain , 1 types, 2 molecules IJ
#6: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97319 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97319 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.67→50 Å / Num. all: 51813 / Num. obs: 50779 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 49.15 Å2 / Rsym value: 0.1 / Χ2: 1.049 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2cv5 Resolution: 2.67→48.667 Å / FOM work R set: 0.8163 / SU ML: 0.42 / σ(F): 1.48 / Phase error: 26.34 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.69 Å2 / Biso mean: 55.43 Å2 / Biso min: 13.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→48.667 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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